Contacts of the helix formed by residues 16 - 37 (chain F) in PDB entry 3ZO7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 16 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F ASN 3.2 6.5 + - - +
15F LEU* 1.3 72.3 - - - +
17F PRO* 1.3 69.5 - - - +
18F ARG* 2.6 56.4 + - - +
19F GLU* 2.6 42.1 + - + +
20F GLU 3.0 8.7 + - - -
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Residues in contact with PRO 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU 3.3 9.4 - - - +
16F ASP* 1.3 89.8 - - - +
18F ARG* 1.3 60.4 + - + +
19F GLU 3.3 0.2 - - - -
20F GLU* 3.7 17.0 - - + +
21F GLU* 3.0 23.6 + - - +
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ASP* 2.6 45.0 + - - +
17F PRO* 1.3 79.0 - - + +
19F GLU* 1.3 64.2 + - - +
21F GLU* 3.2 6.3 + - - +
22F ARG* 3.2 34.0 + - - +
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 3.3 30.2 - - + +
16F ASP* 2.6 28.3 + - + +
18F ARG* 1.3 76.9 - - - +
20F GLU* 1.3 54.3 + - - +
22F ARG* 3.5 24.9 + - - +
23F LEU* 2.9 36.4 + - + +
76F TYR* 4.3 7.6 + - - +
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Residues in contact with GLU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 3.3 31.1 - - + +
15F LEU* 3.8 21.1 - - + +
16F ASP 3.0 8.5 + - - +
17F PRO* 3.7 18.0 - - + +
18F ARG 3.2 0.2 - - - -
19F GLU* 1.3 75.0 - - - +
21F GLU* 1.3 58.6 + - - +
23F LEU* 3.2 6.6 + - + +
24F LYS* 2.8 30.9 + - + +
50F TYR* 4.0 18.2 + - - +
73F PHE* 5.3 2.2 - - + -
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Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F PRO 3.0 13.4 + - - +
18F ARG* 3.2 10.3 + - - +
20F GLU* 1.3 77.7 - - - +
22F ARG* 1.3 62.5 + - - +
24F LYS* 3.1 39.4 + - - +
25F ALA* 2.9 25.2 + - + +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 3.2 22.0 + - - +
19F GLU* 3.7 35.8 - - - +
21F GLU* 1.3 78.7 - - - +
23F LEU* 1.3 63.5 + - - +
25F ALA* 3.3 6.4 + - - +
26F SER* 2.9 36.6 + - - +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.5 4.9 - - + -
15F LEU* 4.7 9.0 - - + -
19F GLU* 2.9 24.0 + - + +
20F GLU* 3.4 6.7 - - - +
21F GLU 3.2 0.2 - - - -
22F ARG* 1.3 77.9 - - - +
24F LYS* 1.3 56.5 + - - +
26F SER* 3.4 5.0 + - - -
27F ALA* 2.9 31.3 + - - +
72F PRO* 3.6 28.9 - - + +
73F PHE* 3.5 32.5 - - + -
75F PRO* 6.4 0.2 - - + -
76F TYR* 3.5 32.5 - - + +
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Residues in contact with LYS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLU* 2.8 21.9 + - + +
21F GLU* 3.4 28.5 + - - +
23F LEU* 1.3 72.6 - - - +
25F ALA* 1.3 83.5 + - - +
27F ALA* 3.4 2.1 + - - +
28F LYS* 2.9 46.6 + - + +
50F TYR* 5.3 6.5 - - - +
73F PHE* 4.3 16.5 - - + -
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLU* 2.9 16.8 + - + +
22F ARG* 3.7 7.2 - - - +
24F LYS* 1.3 90.3 - - - +
26F SER* 1.3 61.1 + - - +
28F LYS* 3.3 5.1 + - - +
29F ALA* 2.9 31.8 + - - +
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Residues in contact with SER 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ARG* 2.9 26.9 + - - +
23F LEU* 3.7 4.7 - - - -
25F ALA* 1.3 76.2 - - - +
27F ALA* 1.3 58.3 + - - +
29F ALA* 3.4 5.3 + - - +
30F ARG* 2.8 31.4 + - - +
72F PRO* 3.7 18.7 - - - +
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Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F LEU 2.9 18.1 + - - +
24F LYS 3.6 3.4 - - - +
26F SER* 1.3 77.4 - - - +
28F LYS* 1.3 57.6 + - - +
30F ARG* 3.2 1.4 + - - +
31F SER* 2.8 32.6 + - - -
72F PRO* 3.6 18.4 - - + +
73F PHE* 3.6 31.4 - - + -
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Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F LYS* 2.9 36.8 + - + +
25F ALA* 3.6 6.3 - - - +
27F ALA* 1.3 75.7 - - - +
29F ALA* 1.3 59.3 + - - +
31F SER* 3.0 19.7 + - - +
32F ARG* 3.0 23.8 + - + +
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Residues in contact with ALA 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ALA 2.9 17.2 + - - +
26F SER* 3.8 6.1 - - - +
28F LYS* 1.3 76.7 - - - +
30F ARG* 1.3 61.8 + - - +
32F ARG* 3.4 9.6 + - - +
33F THR* 3.4 23.7 + - - -
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Residues in contact with ARG 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F SER 2.8 18.5 + - - +
27F ALA 3.6 3.6 - - - +
29F ALA* 1.3 77.8 - - - +
31F SER* 1.3 62.5 + - - +
33F THR* 3.4 18.0 + - - +
34F LEU* 3.2 65.7 + - + +
67F ILE* 4.6 9.9 - - - +
70F SER* 2.9 34.0 + - - +
71F LEU* 4.4 7.4 - - + -
72F PRO* 4.2 22.9 - - + -
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Residues in contact with SER 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA 2.8 15.5 + - - -
28F LYS* 3.0 21.3 + - - +
30F ARG* 1.3 74.1 - - - +
32F ARG* 1.3 64.5 + - - +
34F LEU* 3.3 1.0 + - - +
35F GLN* 2.9 45.5 + - - +
40F TRP* 3.6 35.9 - - - -
43F LEU* 4.8 6.0 - - - +
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Residues in contact with ARG 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F LYS* 3.0 25.5 + - + +
29F ALA* 3.6 9.6 - - - +
30F ARG 3.2 0.4 - - - -
31F SER* 1.3 78.2 + - - +
33F THR* 1.3 60.4 + - - +
35F GLN* 3.3 9.6 + - - +
36F GLU* 2.9 64.0 + - + +
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Residues in contact with THR 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ALA 3.4 10.0 + - - -
30F ARG* 3.4 21.9 + - - +
32F ARG* 1.3 82.3 - - - +
34F LEU* 1.3 64.8 + - + +
36F GLU* 3.2 8.9 + - - +
37F GLN* 3.0 39.5 + - + +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ARG* 3.2 60.6 + - + +
31F SER 3.9 3.6 - - - +
33F THR* 1.3 80.8 - - + +
35F GLN* 1.3 58.5 + - - +
37F GLN* 3.8 0.6 + - - -
38F GLY 3.2 2.3 + - - -
39F GLN* 3.0 46.3 + - + +
40F TRP* 3.0 32.8 + - + +
56F PHE* 5.4 0.2 - - + -
67F ILE* 3.9 43.5 - - + -
71F LEU* 4.3 4.9 - - + -
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Residues in contact with GLN 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F SER* 2.9 38.8 + - - +
32F ARG* 3.6 8.4 - - - +
34F LEU* 1.3 75.7 - - - +
36F GLU* 1.3 64.9 + - + +
38F GLY* 3.0 14.4 + - - -
40F TRP* 3.4 34.0 - - + +
41F ARG* 5.4 2.6 - - - +
42F TYR 5.6 0.2 - - - -
43F LEU* 3.7 36.6 + - - +
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Residues in contact with GLU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ARG* 2.9 57.2 + - + +
33F THR* 3.2 7.9 + - - +
35F GLN* 1.3 78.0 - - + +
37F GLN* 1.3 75.5 + - - +
38F GLY* 3.5 0.9 + - - -
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F THR* 3.0 27.9 + - + +
34F LEU 4.4 0.2 - - - +
36F GLU* 1.3 95.8 + - - +
38F GLY* 1.3 60.0 + - - +
39F GLN* 3.4 23.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il